[English] 日本語
Yorodumi
- PDB-5vu2: Electron cryo-microscopy of "immature" Chikungunya VLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vu2
TitleElectron cryo-microscopy of "immature" Chikungunya VLP
Components
  • (E1 envelope glycoprotein) x 2
  • E2 envelope glycoprotein
  • E3 envelope glycoprotein
  • capsid protein
KeywordsVIRUS LIKE PARTICLE / Chikungunya / virus / immature
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus strain Senegal 37997
Chikungunya virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å
AuthorsRossmann, M.G. / Yap, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095366 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural studies of Chikungunya virus maturation.
Authors: Moh Lan Yap / Thomas Klose / Akane Urakami / S Saif Hasan / Wataru Akahata / Michael G Rossmann /
Abstract: Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. ...Cleavage of the alphavirus precursor glycoprotein p62 into the E2 and E3 glycoproteins before assembly with the nucleocapsid is the key to producing fusion-competent mature spikes on alphaviruses. Here we present a cryo-EM, 6.8-Å resolution structure of an "immature" Chikungunya virus in which the cleavage site has been mutated to inhibit proteolysis. The spikes in the immature virus have a larger radius and are less compact than in the mature virus. Furthermore, domains B on the E2 glycoproteins have less freedom of movement in the immature virus, keeping the fusion loops protected under domain B. In addition, the nucleocapsid of the immature virus is more compact than in the mature virus, protecting a conserved ribosome-binding site in the capsid protein from exposure. These differences suggest that the posttranslational processing of the spikes and nucleocapsid is necessary to produce infectious virus.
History
DepositionMay 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-8734
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8734
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)911,44424
Polymers911,44424
Non-polymers00
Water00
1
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 60


Theoretical massNumber of molelcules
Total (without water)54,686,6421440
Polymers54,686,6421440
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 5


  • icosahedral pentamer
  • 4.56 MDa, 120 polymers
Theoretical massNumber of molelcules
Total (without water)4,557,220120
Polymers4,557,220120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
M: E1 envelope glycoprotein
A: E1 envelope glycoprotein
U: E3 envelope glycoprotein
V: E3 envelope glycoprotein
B: E1 envelope glycoprotein
N: E1 envelope glycoprotein
W: E3 envelope glycoprotein
C: E1 envelope glycoprotein
O: E1 envelope glycoprotein
X: E3 envelope glycoprotein
D: E1 envelope glycoprotein
P: E1 envelope glycoprotein
I: capsid protein
J: capsid protein
K: capsid protein
L: capsid protein
E: E1 envelope glycoprotein
Q: E2 envelope glycoprotein
F: E1 envelope glycoprotein
R: E2 envelope glycoprotein
G: E1 envelope glycoprotein
S: E2 envelope glycoprotein
H: E1 envelope glycoprotein
T: E2 envelope glycoprotein
x 6


  • icosahedral 23 hexamer
  • 5.47 MDa, 144 polymers
Theoretical massNumber of molelcules
Total (without water)5,468,664144
Polymers5,468,664144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Protein
E1 envelope glycoprotein


Mass: 95538.164 Da / Num. of mol.: 8 / Fragment: UNP residues 326-1191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: A0A0H4CWF2
#2: Protein
E3 envelope glycoprotein


Mass: 6926.990 Da / Num. of mol.: 4 / Fragment: UNP residues 266-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Gene: CHIKVgp2 / Production host: Homo sapiens (human) / References: UniProt: C7S7A1, UniProt: Q5XXP3*PLUS
#3: Protein
capsid protein


Mass: 16229.508 Da / Num. of mol.: 4 / Fragment: UNP residues 113-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus (strain 37997) / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#4: Protein/peptide
E1 envelope glycoprotein


Mass: 4810.723 Da / Num. of mol.: 4 / Fragment: transmembrane helix (UNP residues 1203-1248)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
#5: Protein
E2 envelope glycoprotein


Mass: 8817.458 Da / Num. of mol.: 4 / Fragment: transmembrane helix (UNP residues 668-748)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus strain Senegal 37997 / Strain: 37997 / Production host: Homo sapiens (human) / References: UniProt: Q5XXP3
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Chikungunya virus strain Senegal 37997 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Chikungunya virus strain Senegal 37997
Source (recombinant)Organism: Homo sapiens (human) / Cell: Human embryonic kidney / Plasmid: pUC119
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameCategory
2Leginonimage acquisition
7EMfitmodel fitting
13jspr3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72944 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more